The study of organelle genes and genomes is essential to our understand- ing of eukaryotic cellular and molecular biology. The proper functioning of organelles in all eukaryotic cells involves a precise cooperation between nuclear and organelle genetic systems. Defects in this functioning have direct consequences for human health, as is evident from the recent explosion of reports on mitochondrially-inherited diseases. This proposal addresses the fundamental problem in the genetic coevolut- ion of the eukaryotic cell: How are organellar genes functionally transferred to the nucleus and what are the consequences of these genetic relocations? First, several cases of recent gene transfer will be explored in order to 1) gain insights into the timing and process of functional activation of a transferred organellar gene within the nucleus; 2) examine the prevalence of RNA intermediates and reverse transcription in the physical act of sequence migration between cellular compartments; and 3) test the hypothesis that spliceosomal-dependent nuclear pre-MRNA introns evolved from self-splicing group II introns. Second, a more ancient transfer to the nucleus, of the chloroplast gene tufA, will be examined to test two hypotheses relating to gene function: 1) that this gene transfer allowed, in the green alga Coleochaete, a novel situation of cross-compartmental gene amplification, with functional divergence among the gene copies, and 2) that this same transfer, in the land plant Arabidopsis, resulted in the nearly opposite (and also novel) situation, whereby one nuclear gene supplies both the chloroplast and mitochondrion with the same protein. Finally, we will continue to study, using a variety of molecular evolutionary approaches, the dramatically accelerated molecular evolution of the chloroplast-encoded RNA polymerase in geranium.